1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
|
# Copyright 1999 by Jeffrey Chang. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
import string
import sys
from Bio import File
from Bio import ParserSupport
# pyUnit
def pb(b):
if b:
return 1
return 0
### TaggingConsumer
print "Running tests on TaggingConsumer"
class TestHandle:
def write(self, s):
print s
h = TestHandle()
tc = ParserSupport.TaggingConsumer(handle=h, colwidth=5)
tc.start_section() # '***** start_section\n'
tc.test1('myline') # 'test1: myline\n'
tc.end_section() # '***** end_section\n'
### is_blank_line
print "Running tests on is_blank_line"
is_blank_line = lambda *args, **keywds: \
pb(ParserSupport.is_blank_line(*args, **keywds))
print is_blank_line('\n') # 1
print is_blank_line('\r\n') # 1
print is_blank_line('\r') # 1
print is_blank_line('') # 1
print is_blank_line('', allow_spaces=1) # 1
print is_blank_line('', allow_spaces=0) # 1
print is_blank_line(string.whitespace, allow_spaces=1) # 1
print is_blank_line('hello') # 0
print is_blank_line('hello', allow_spaces=1) # 0
print is_blank_line('hello', allow_spaces=0) # 0
print is_blank_line(string.whitespace, allow_spaces=0) # 0
### safe_readline
print "Running tests on safe_readline"
data = """This
file"""
h = File.UndoHandle(File.StringHandle(data))
safe_readline = ParserSupport.safe_readline
print safe_readline(h) # "This"
print safe_readline(h) # "file"
try: safe_readline(h)
except ValueError: print "correctly failed"
else: print "ERROR, should have failed"
### safe_peekline
print "Running tests on safe_peekline"
safe_peekline = ParserSupport.safe_peekline
data = """This
file"""
h = File.UndoHandle(File.StringHandle(data))
print safe_peekline(h) # "This"
h.readline()
print safe_peekline(h) # "file"
h.readline()
try: safe_peekline(h)
except ValueError: print "correctly failed"
else: print "ERROR, should have failed"
h.saveline('hello')
print safe_peekline(h) # 'hello'
### read_and_call
print "Running tests on read_and_call"
data = """>gi|132871|sp|P19947|RL30_BACSU 50S RIBOSOMAL PROTEIN L30 (BL27)
MAKLEITLKRSVIGRPEDQRVTVRTLGLKKTNQTVVHEDNAAIRGMINKVSHLVSVKEQ
>gi|132679|sp|P19946|RL15_BACSU 50S RIBOSOMAL PROTEIN L15
MKLHELKPSEGSRKTRNRVGRGIGSGNGKTAGKGHKGQNARSGGGVRPGFEGGQMPLFQRLPKRGFTNIN
RKEYAVVNLDKLNGFAEGTEVTPELLLETGVISKLNAGVKILGNGKLEKKLTVKANKFSASAKEAVEAAG
GTAEVI
"""
h = File.UndoHandle(File.StringHandle(data))
rac = ParserSupport.read_and_call
lines = []
def m(line):
lines.append(line)
rac(h, m)
print lines[-1][:10] # '>gi|132871'
rac(h, m, start='MAKLE', end='KEQ', contains='SVIG')
rac(h, m, blank=0)
# These should be errors. If they're not, then complain.
try: rac(h, m, blank=1)
except ValueError: print "correctly failed"
else: print "ERROR, should have failed"
try: rac(h, m, start='foobar')
except ValueError: print "correctly failed"
else: print "ERROR, should have failed"
try: rac(h, m, end='foobar')
except ValueError: print "correctly failed"
else: print "ERROR, should have failed"
try: rac(h, m, contains='foobar')
except ValueError: print "correctly failed"
else: print "ERROR, should have failed"
try: rac(h, m, blank=0)
except ValueError: print "correctly failed"
else: print "ERROR, should have failed"
### attempt_read_and_call
print "Running tests on attempt_read_and_call"
data = """>gi|132871|sp|P19947|RL30_BACSU 50S RIBOSOMAL PROTEIN L30 (BL27)
MAKLEITLKRSVIGRPEDQRVTVRTLGLKKTNQTVVHEDNAAIRGMINKVSHLVSVKEQ
>gi|132679|sp|P19946|RL15_BACSU 50S RIBOSOMAL PROTEIN L15
MKLHELKPSEGSRKTRNRVGRGIGSGNGKTAGKGHKGQNARSGGGVRPGFEGGQMPLFQRLPKRGFTNIN
RKEYAVVNLDKLNGFAEGTEVTPELLLETGVISKLNAGVKILGNGKLEKKLTVKANKFSASAKEAVEAAG
GTAEVI"""
h = File.UndoHandle(File.StringHandle(data))
arac = lambda *args, **keywds: \
pb(ParserSupport.attempt_read_and_call(*args, **keywds))
lines = []
def m(line):
lines.append(line)
print arac(h, m, contains="RIBOSOMAL PROTEIN") # 1
print arac(h, m, start="foobar") # 0
print arac(h, m, blank=1) # 0
print arac(h, m, end="LVSVKEQ") # 1
|
